There is only one way to manage those malcontents.

Build a large garrison, then leave the city. When they declare their independence, you declare war on them and lay seige. Then when you take the city back, sack it. If it happens again, exterminate them.

Use your pillaging florins to rebuild your vital garrisons and city walls, and let the rebellious fools return to their farmery. Raising crops is for the weak and enslaved anyway.